{"payload":{"pageCount":1,"repositories":[{"type":"Public","name":"acdc_py","owner":"califano-lab","isFork":false,"description":"scanpy-compatible suite for automated clustering of scRNA-seq data in python","allTopics":["python","bioinformatics","clustering","single-cell-rna-seq"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-09-10T19:04:16.887Z"}},{"type":"Public","name":"MAPK_Experimental_Signature","owner":"califano-lab","isFork":false,"description":"This repository contains an example of code to generate a MAPK Experimental Signature from PlateSeq data","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-08-30T21:14:13.265Z"}},{"type":"Public","name":"vespa.tutorial","owner":"califano-lab","isFork":false,"description":"Tutorials on how to use the VESPA algorithm","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T10:35:00.730Z"}},{"type":"Public","name":"vespa.net","owner":"califano-lab","isFork":false,"description":"VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) signaling network inference module","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T10:34:27.698Z"}},{"type":"Public","name":"vespa.db","owner":"califano-lab","isFork":false,"description":"VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) supplementary data package","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T10:34:00.674Z"}},{"type":"Public","name":"vespa.aracne","owner":"califano-lab","isFork":false,"description":"VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) ARACNe module","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T10:33:26.530Z"}},{"type":"Public","name":"vespa","owner":"califano-lab","isFork":false,"description":"VESPA (Virtual Enrichment-based Signaling Protein-activity Analysis) algorithm","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-03-01T10:32:28.884Z"}},{"type":"Public","name":"acdc","owner":"califano-lab","isFork":false,"description":"suite for clustering of scRNA-seq data (beta version)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-06-11T21:57:29.191Z"}},{"type":"Public","name":"ARACNe-AP","owner":"califano-lab","isFork":false,"description":"Network Reverse Engineering through AP inference of Mutual Information","allTopics":[],"primaryLanguage":{"name":"Java","color":"#b07219"},"pullRequestCount":2,"issueCount":14,"starsCount":81,"forksCount":24,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-06T16:48:35.016Z"}},{"type":"Public","name":"NaRnEA","owner":"califano-lab","isFork":false,"description":"NaRnEA (Nonparametric analytical Rank-based Enrichment Analysis)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":9,"forksCount":4,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-02T15:19:30.090Z"}},{"type":"Public","name":"Olive_926-mouse-screen","owner":"califano-lab","isFork":false,"description":"LJV analysis code for IPI 926 mouse drug screening data from the Olive lab.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-28T23:52:11.268Z"}},{"type":"Public","name":"NDP-KO-SC","owner":"califano-lab","isFork":false,"description":"Analysis code for collaboration with the Kuo lab. Single-cell analysis of NDP KO mice w/ and w/ out L6-F4-2 therapeutic agent.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-16T22:00:54.537Z"}},{"type":"Public","name":"PISCES","owner":"califano-lab","isFork":false,"description":"R package for Protein activity analysis of single-cell RNAseq.","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":1,"issueCount":19,"starsCount":75,"forksCount":24,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-15T17:35:08.470Z"}},{"type":"Public","name":"SHARP-SCABC-2022","owner":"califano-lab","isFork":false,"description":"Hands-on session code and data from the 2022 SHARP Single Cell Analysis Boot Camp.","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-07-27T18:14:22.247Z"}},{"type":"Public","name":"MOMA","owner":"califano-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":6,"forksCount":3,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-04-09T18:36:13.345Z"}},{"type":"Public","name":"Statistical_Rethinking_with_brms_ggplot2_and_the_tidyverse_2_ed","owner":"califano-lab","isFork":true,"description":"The bookdown version lives here:","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":37,"license":"Creative Commons Zero v1.0 Universal","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2021-03-26T14:14:02.125Z"}},{"type":"Public","name":"OncoSig","owner":"califano-lab","isFork":false,"description":"Code to run OncoSig Analyses","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":18,"forksCount":5,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-09-30T15:58:43.698Z"}},{"type":"Public","name":"SEARCHIN","owner":"califano-lab","isFork":true,"description":"Systematic Elucidation and Assessment of Regulatory Cell-to-cell Interaction Networks (SEARCHIN)","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":3,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-09-18T20:29:32.393Z"}},{"type":"Public","name":"COSMA","owner":"califano-lab","isFork":false,"description":"Final code for the cosma collaboration (for paper submission).","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-06-06T00:06:58.640Z"}},{"type":"Public","name":"moma.gbmexample","owner":"califano-lab","isFork":false,"description":"Example gbm multi-omic data for moma package vignette","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-04-03T18:21:41.003Z"}},{"type":"Public","name":"single-cell-pipeline","owner":"califano-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":1,"issueCount":11,"starsCount":40,"forksCount":8,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2020-01-16T17:31:34.147Z"}},{"type":"Public","name":"GTEx-Networks","owner":"califano-lab","isFork":false,"description":"Tissue specific network for GTEx tissue data (TPM normalized).","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-10-14T17:57:49.376Z"}},{"type":"Public","name":"gbm-multiomic-data","owner":"califano-lab","isFork":false,"description":"Data for the MOMA Bioconductor package","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-09-11T15:54:54.670Z"}},{"type":"Public","name":"CZI","owner":"califano-lab","isFork":false,"description":"CZI Project Results","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-04-15T19:39:40.340Z"}},{"type":"Public","name":"ADVOCATE","owner":"califano-lab","isFork":false,"description":"ADVOCATE ","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":2,"starsCount":3,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2019-01-31T14:50:15.732Z"}},{"type":"Public","name":"tf_cotf_signalling_list","owner":"califano-lab","isFork":false,"description":"The list of TFs, coTFs, signalling, surfaceMarkers, etc for ARACNe","allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-11-28T21:32:27.885Z"}},{"type":"Public","name":"scPLATE-Seq","owner":"califano-lab","isFork":false,"description":"","allTopics":[],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2018-07-26T17:37:34.993Z"}},{"type":"Public","name":"DeMAND-algorithm","owner":"califano-lab","isFork":true,"description":"The Drug Mechanism of Action Algorithm Developed in the Califano Lab","allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":6,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-10-25T17:27:22.952Z"}},{"type":"Public","name":"GPU-ARACNE","owner":"califano-lab","isFork":false,"description":"GPU-ARACNE","allTopics":[],"primaryLanguage":{"name":"Cuda","color":"#3A4E3A"},"pullRequestCount":0,"issueCount":1,"starsCount":2,"forksCount":1,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2017-03-29T03:54:49.751Z"}}],"repositoryCount":29,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"califano-lab repositories"}